Mercurial > hg > orthanc-wsi
annotate Framework/Inputs/DicomPyramidInstance.cpp @ 218:c5a8b46c4cba
Fix colorspace of TIFF containing JPEG with RGB photometric interpretation
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 12 Jan 2021 16:20:57 +0100 |
parents | 20bc074ec19a |
children | ef3f8c5126a4 |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
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22 #include "../PrecompiledHeadersWSI.h" |
0 | 23 #include "DicomPyramidInstance.h" |
24 | |
194 | 25 #include "../DicomToolbox.h" |
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26 #include "../../Resources/Orthanc/Stone/DicomDatasetReader.h" |
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27 #include "../../Resources/Orthanc/Stone/FullOrthancDataset.h" |
194 | 28 |
192 | 29 #include <Logging.h> |
30 #include <OrthancException.h> | |
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31 #include <SerializationToolbox.h> |
192 | 32 #include <Toolbox.h> |
33 | |
0 | 34 #include <cassert> |
35 | |
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36 #define SERIALIZED_METADATA "4201" // Was "4200" if versions <= 0.7 of this plugin |
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37 |
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38 |
0 | 39 namespace OrthancWSI |
40 { | |
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41 static const Orthanc::DicomTag DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021e); |
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42 static const Orthanc::DicomTag DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE(0x5200, 0x9230); |
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43 static const Orthanc::DicomTag DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE(0x0048, 0x021a); |
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44 static const Orthanc::DicomTag DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX(0x0048, 0x021f); |
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45 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS(0x0048, 0x0006); |
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46 static const Orthanc::DicomTag DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS(0x0048, 0x0007); |
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47 |
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48 static ImageCompression DetectImageCompression(OrthancStone::IOrthancConnection& orthanc, |
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49 const std::string& instanceId) |
0 | 50 { |
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51 using namespace OrthancStone; |
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52 |
87 | 53 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/header"); |
54 DicomDatasetReader header(dataset); | |
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55 |
0 | 56 std::string s = Orthanc::Toolbox::StripSpaces |
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57 (header.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_TRANSFER_SYNTAX_UID))); |
0 | 58 |
59 if (s == "1.2.840.10008.1.2" || | |
60 s == "1.2.840.10008.1.2.1") | |
61 { | |
62 return ImageCompression_None; | |
63 } | |
64 else if (s == "1.2.840.10008.1.2.4.50") | |
65 { | |
66 return ImageCompression_Jpeg; | |
67 } | |
68 else if (s == "1.2.840.10008.1.2.4.90" || | |
69 s == "1.2.840.10008.1.2.4.91") | |
70 { | |
71 return ImageCompression_Jpeg2000; | |
72 } | |
73 else | |
74 { | |
75 LOG(ERROR) << "Unsupported transfer syntax: " << s; | |
76 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); | |
77 } | |
78 } | |
79 | |
80 | |
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81 static void DetectPixelFormat(Orthanc::PixelFormat& format, |
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82 Orthanc::PhotometricInterpretation& photometric, |
216 | 83 const OrthancStone::DicomDatasetReader& reader) |
0 | 84 { |
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85 using namespace OrthancStone; |
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86 |
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87 std::string p = Orthanc::Toolbox::StripSpaces |
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88 (reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_PHOTOMETRIC_INTERPRETATION))); |
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89 |
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90 photometric = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
0 | 91 |
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92 if (photometric == Orthanc::PhotometricInterpretation_Palette) |
0 | 93 { |
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94 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, |
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95 "Unsupported photometric interpretation: " + p); |
0 | 96 } |
97 | |
89 | 98 unsigned int bitsStored, samplesPerPixel, tmp; |
99 | |
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100 if (!reader.GetUnsignedIntegerValue(bitsStored, OrthancStone::DicomPath(Orthanc::DICOM_TAG_BITS_STORED)) || |
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101 !reader.GetUnsignedIntegerValue(samplesPerPixel, OrthancStone::DicomPath(Orthanc::DICOM_TAG_SAMPLES_PER_PIXEL)) || |
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102 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_PIXEL_REPRESENTATION))) |
89 | 103 { |
104 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); | |
105 } | |
106 | |
107 bool isSigned = (tmp != 0); | |
0 | 108 |
109 if (bitsStored == 8 && | |
110 samplesPerPixel == 1 && | |
111 !isSigned) | |
112 { | |
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113 format = Orthanc::PixelFormat_Grayscale8; |
0 | 114 } |
115 else if (bitsStored == 8 && | |
116 samplesPerPixel == 3 && | |
117 !isSigned) | |
118 { | |
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119 format = Orthanc::PixelFormat_RGB24; |
0 | 120 } |
121 else | |
122 { | |
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123 throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "Unsupported pixel format"); |
0 | 124 } |
125 } | |
126 | |
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127 |
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128 ImageCompression DicomPyramidInstance::GetImageCompression(OrthancStone::IOrthancConnection& orthanc) |
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129 { |
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130 /** |
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131 * Lazy detection of the image compression using the transfer |
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132 * syntax stored inside the DICOM header. Given the fact that |
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133 * reading the header is a time-consuming operation (it implies |
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134 * the decoding of the DICOM image by Orthanc, whereas the "/tags" |
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135 * endpoint only reads the "DICOM-as-JSON" attachment), the |
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136 * "/header" REST call is delayed until it is really required. |
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137 **/ |
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138 |
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139 if (!hasCompression_) |
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140 { |
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141 compression_ = DetectImageCompression(orthanc, instanceId_); |
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142 hasCompression_ = true; |
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143 } |
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144 |
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145 return compression_; |
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146 } |
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147 |
0 | 148 |
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149 void DicomPyramidInstance::Load(OrthancStone::IOrthancConnection& orthanc, |
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150 const std::string& instanceId) |
0 | 151 { |
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152 using namespace OrthancStone; |
0 | 153 |
87 | 154 FullOrthancDataset dataset(orthanc, "/instances/" + instanceId + "/tags"); |
155 DicomDatasetReader reader(dataset); | |
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156 |
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157 if (reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_SOP_CLASS_UID)) != "1.2.840.10008.5.1.4.1.1.77.1.6" || |
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158 reader.GetMandatoryStringValue(OrthancStone::DicomPath(Orthanc::DICOM_TAG_MODALITY)) != "SM") |
0 | 159 { |
160 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); | |
161 } | |
162 | |
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163 hasCompression_ = false; |
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164 DetectPixelFormat(format_, photometric_, reader); |
89 | 165 |
166 unsigned int tmp; | |
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167 if (!reader.GetUnsignedIntegerValue(tileWidth_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_COLUMNS)) || |
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168 !reader.GetUnsignedIntegerValue(tileHeight_, OrthancStone::DicomPath(Orthanc::DICOM_TAG_ROWS)) || |
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169 !reader.GetUnsignedIntegerValue(totalWidth_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_COLUMNS)) || |
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170 !reader.GetUnsignedIntegerValue(totalHeight_, OrthancStone::DicomPath(DICOM_TAG_TOTAL_PIXEL_MATRIX_ROWS)) || |
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171 !reader.GetUnsignedIntegerValue(tmp, OrthancStone::DicomPath(Orthanc::DICOM_TAG_NUMBER_OF_FRAMES))) |
89 | 172 { |
173 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); | |
174 } | |
0 | 175 |
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176 size_t countFrames; |
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177 if (reader.GetDataset().GetSequenceSize(countFrames, OrthancStone::DicomPath(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE))) |
0 | 178 { |
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179 if (countFrames != tmp) |
89 | 180 { |
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181 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
0 | 182 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
183 } | |
184 | |
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185 frames_.resize(countFrames); |
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186 |
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187 for (size_t i = 0; i < countFrames; i++) |
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188 { |
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189 DicomPath pathX(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
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190 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, |
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191 DICOM_TAG_COLUMN_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); |
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192 |
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193 DicomPath pathY(DICOM_TAG_PER_FRAME_FUNCTIONAL_GROUPS_SEQUENCE, i, |
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194 DICOM_TAG_PLANE_POSITION_SLIDE_SEQUENCE, 0, |
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195 DICOM_TAG_ROW_POSITION_IN_TOTAL_IMAGE_PIXEL_MATRIX); |
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196 |
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197 int xx, yy; |
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198 if (!reader.GetIntegerValue(xx, pathX) || |
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199 !reader.GetIntegerValue(yy, pathY)) |
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200 { |
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201 throw Orthanc::OrthancException(Orthanc::ErrorCode_InexistentTag); |
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202 } |
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203 |
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204 // "-1", because coordinates are shifted by 1 in DICOM |
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205 xx -= 1; |
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206 yy -= 1; |
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207 |
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208 unsigned int x = static_cast<unsigned int>(xx); |
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209 unsigned int y = static_cast<unsigned int>(yy); |
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210 |
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211 if (xx < 0 || |
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212 yy < 0 || |
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213 x % tileWidth_ != 0 || |
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214 y % tileHeight_ != 0 || |
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215 x >= totalWidth_ || |
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216 y >= totalHeight_) |
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217 { |
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218 LOG(ERROR) << "Frame " << i << " with unexpected tile location (" |
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219 << x << "," << y << ") in instance: " << instanceId; |
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220 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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221 } |
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222 |
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223 frames_[i].first = x / tileWidth_; |
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224 frames_[i].second = y / tileHeight_; |
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225 } |
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226 } |
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227 else |
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228 { |
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229 // No "Per frame functional groups sequence" tag. Assume regular grid. |
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230 frames_.resize(tmp); |
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231 |
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232 // Compute "ceiling(totalWidth_ / tileWidth_) |
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233 unsigned int w = totalWidth_ / tileWidth_; |
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234 if (totalWidth_ % tileWidth_ != 0) |
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235 { |
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236 w += 1; |
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237 } |
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238 |
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239 unsigned int h = totalHeight_ / tileHeight_; |
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240 if (totalHeight_ % tileHeight_ != 0) |
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241 { |
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242 h += 1; |
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243 } |
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244 |
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245 if (w * h != tmp) |
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246 { |
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247 LOG(ERROR) << "Mismatch between the number of frames in instance: " << instanceId; |
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248 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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249 } |
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250 |
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251 for (size_t i = 0; i < frames_.size(); i++) |
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252 { |
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253 frames_[i].first = i % w; |
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254 frames_[i].second = i / w; |
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255 } |
0 | 256 } |
257 } | |
258 | |
259 | |
196
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260 DicomPyramidInstance::DicomPyramidInstance(OrthancStone::IOrthancConnection& orthanc, |
69
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261 const std::string& instanceId, |
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262 bool useCache) : |
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263 instanceId_(instanceId), |
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264 hasCompression_(false), |
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265 compression_(ImageCompression_None) // Dummy initialization for serialization |
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266 { |
69
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267 if (useCache) |
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268 { |
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269 try |
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270 { |
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271 // Try and deserialized the cached information about this instance |
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272 std::string serialized; |
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273 orthanc.RestApiGet(serialized, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA); |
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274 std::cout << serialized; |
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275 Deserialize(serialized); |
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276 return; // Success |
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277 } |
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278 catch (Orthanc::OrthancException&) |
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279 { |
70 | 280 // No cached information yet |
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281 } |
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282 } |
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283 |
70 | 284 // Compute information about this instance from scratch |
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285 Load(orthanc, instanceId); |
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286 |
70 | 287 if (useCache) |
288 { | |
289 // Serialize the computed information and cache it as a metadata | |
290 std::string serialized, tmp; | |
291 Serialize(serialized); | |
292 orthanc.RestApiPut(tmp, "/instances/" + instanceId + "/metadata/" + SERIALIZED_METADATA, serialized); | |
293 } | |
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294 } |
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295 |
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296 |
0 | 297 unsigned int DicomPyramidInstance::GetFrameLocationX(size_t frame) const |
298 { | |
299 assert(frame < frames_.size()); | |
300 return frames_[frame].first; | |
301 } | |
302 | |
303 | |
304 unsigned int DicomPyramidInstance::GetFrameLocationY(size_t frame) const | |
305 { | |
306 assert(frame < frames_.size()); | |
307 return frames_[frame].second; | |
308 } | |
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309 |
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310 |
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311 |
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312 static const char* const HAS_COMPRESSION = "HasCompression"; |
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313 static const char* const IMAGE_COMPRESSION = "ImageCompression"; |
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314 static const char* const PIXEL_FORMAT = "PixelFormat"; |
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315 static const char* const FRAMES = "Frames"; |
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316 static const char* const TILE_WIDTH = "TileWidth"; |
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317 static const char* const TILE_HEIGHT = "TileHeight"; |
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318 static const char* const TOTAL_WIDTH = "TotalWidth"; |
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319 static const char* const TOTAL_HEIGHT = "TotalHeight"; |
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320 static const char* const PHOTOMETRIC_INTERPRETATION = "PhotometricInterpretation"; |
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321 |
64
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322 |
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323 void DicomPyramidInstance::Serialize(std::string& result) const |
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324 { |
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325 Json::Value frames = Json::arrayValue; |
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326 for (size_t i = 0; i < frames_.size(); i++) |
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327 { |
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328 Json::Value frame = Json::arrayValue; |
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329 frame.append(frames_[i].first); |
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330 frame.append(frames_[i].second); |
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331 frames.append(frame); |
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332 } |
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333 |
217
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334 Json::Value content = Json::objectValue; |
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335 content[FRAMES] = frames; |
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336 |
217
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337 // "instanceId_" is set by the constructor |
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338 |
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339 content[HAS_COMPRESSION] = hasCompression_; |
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340 content[IMAGE_COMPRESSION] = static_cast<int>(compression_); |
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341 content[PIXEL_FORMAT] = static_cast<int>(format_); |
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342 content[TILE_WIDTH] = tileWidth_; |
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343 content[TILE_HEIGHT] = tileHeight_; |
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344 content[TOTAL_WIDTH] = totalWidth_; |
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345 content[TOTAL_HEIGHT] = totalHeight_; |
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346 content[PHOTOMETRIC_INTERPRETATION] = Orthanc::EnumerationToString(photometric_); |
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347 |
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348 Orthanc::Toolbox::WriteFastJson(result, content); |
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349 } |
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350 |
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351 |
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352 void DicomPyramidInstance::Deserialize(const std::string& s) |
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353 { |
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354 Json::Value content; |
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355 Orthanc::Toolbox::ReadJson(content, s); |
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356 |
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357 if (content.type() != Json::objectValue || |
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358 !content.isMember(FRAMES) || |
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359 content[FRAMES].type() != Json::arrayValue) |
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360 { |
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361 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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362 } |
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363 |
217
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364 hasCompression_ = Orthanc::SerializationToolbox::ReadBoolean(content, HAS_COMPRESSION); |
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365 compression_ = static_cast<ImageCompression>(Orthanc::SerializationToolbox::ReadInteger(content, IMAGE_COMPRESSION)); |
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366 format_ = static_cast<Orthanc::PixelFormat>(Orthanc::SerializationToolbox::ReadInteger(content, PIXEL_FORMAT)); |
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367 tileWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_WIDTH); |
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368 tileHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TILE_HEIGHT); |
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369 totalWidth_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_WIDTH); |
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370 totalHeight_ = Orthanc::SerializationToolbox::ReadUnsignedInteger(content, TOTAL_HEIGHT); |
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371 |
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372 std::string p = Orthanc::SerializationToolbox::ReadString(content, PHOTOMETRIC_INTERPRETATION); |
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373 photometric_ = Orthanc::StringToPhotometricInterpretation(p.c_str()); |
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374 |
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375 const Json::Value f = content[FRAMES]; |
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376 frames_.resize(f.size()); |
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377 |
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378 for (Json::Value::ArrayIndex i = 0; i < f.size(); i++) |
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379 { |
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380 if (f[i].type() != Json::arrayValue || |
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381 f[i].size() != 2 || |
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382 f[i][0].type() != Json::intValue || |
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383 f[i][1].type() != Json::intValue || |
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384 f[i][0].asInt() < 0 || |
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385 f[i][1].asInt() < 0) |
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386 { |
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387 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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388 } |
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389 |
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390 frames_[i].first = f[i][0].asInt(); |
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391 frames_[i].second = f[i][1].asInt(); |
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392 } |
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393 } |
0 | 394 } |